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<title>Per Base N Content</title>
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<h1>Per Base N Content</h1>
<h2>Summary</h2>
<p>
If a sequencer is unable to make a base call with sufficient confidence
then it will normally substitute an N rather than a conventional base]
call
</p>
<p>
This module plots out the percentage of base calls at each position for
which an N was called.
</p>
<p><img src="per_base_n_content.png"></p>

<p>
It's not unusual to see a very low proportion of Ns appearing in a sequence, 
especially nearer the end of a sequence.  However, if this proportion rises
above a few percent it suggests that the analysis pipeline was unable to
interpret the data well enough to make valid base calls.
</p>

<h2>Warning</h2>
<p>
This module raises a warning if any position shows an N content of >5%.
</p>

<h2>Failure</h2>
<p>
This module will raise an error if any position shows an N content of >20%.
</p>

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